cosmosR - Githubissues

katharinazirngibl commented 3 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/saezlab/cosmosR

Confirm the following by editing each check box to '[x]'

[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
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bioc-issue-bot commented 3 years ago

Hi @katharinazirngibl

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: cosmosR
Type: Package
Title: COSMOS (Causal Oriented Search of Multi-Omic Space)
Version: 0.99.0
Description: COSMOS (Causal Oriented Search of Multi-Omic Space) is a method 
    that integrates phosphoproteomics, transcriptomics, and metabolomics data sets
    based on prior knowledge of signaling, metabolic, and gene regulatory
    networks. It estimated the activities of transcrption factors and kinases
    and finds a network-level causal reasoning. Thereby, COSMOS provides 
    mechanistic hypotheses for experimental observations across mulit-omics datasets.
Authors@R: c(
    person(given = "Aurélien",
 family = "Dugourd",
 role = c("aut"),
 email = "dugourdaurelien@gmail.com",
 comment = c(ORCID = "0000-0002-0714-028X")),
    person(given = "Attila",
 family = "Gabor",
 role = c("aut"),
 email = "attila.gabor@uni-heidelberg.de",
 comment = c(ORCID = "0000-0002-0776-1182")),
    person(given = "Katharina",
 family = "Zirngibl",
 role = c("cre","aut"),
 email = "katharina.zirngibl@uni-heidelberg.de",
 comment = c(ORCID = "0000-0002-7518-0339")))
URL: https://github.com/saezlab/COSMOS
BugReports: https://github.com/saezlab/COSMOS/issues
Depends: R (>= 4.0)
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Imports:
    CARNIVAL,
    dorothea,
    igraph,
    dplyr,
    stringr,
    readr,
    rlang,
    tibble,
    purrr,
    AnnotationDbi,
    biomaRt,
    org.Hs.eg.db,
    visNetwork
Suggests: 
    testthat,
    knitr,
    rmarkdown
biocViews: CellBiology, Pathways, Network, Proteomics, Metabolomics, Transcriptomics,
    GeneSignaling

bioc-issue-bot commented 3 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/cosmosR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d3a0bf3da67df5c9175cedeeeeddb8561088cacc

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/cosmosR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6125ec2f67b3de8821bdc69ba5261564bed2b700

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/cosmosR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Kayla-Morrell commented 3 years ago

@katharinazirngibl - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

General package development

[ ] REQUIRED: The 'docs/' directory should be removed, this isn't something we allow in Bioconductor packages.

DESCRIPTION

[ ] REQUIRED: Since you are using a standard library, you don't need to use the LICENSE file and it should be removed.
[ ] REQUIRED: 'LazyData:' in the DESCRIPTION file should be set to false or removed.

NEWS

[ ] REQUIRED: It's great practice to include a NEWS file but it looks like yours is not formatted properly. Please take a look at our documentation here and reformat the file.

Vignette

[ ] REQUIRED: Add an "Installation" section that demonstrates to the user how to download the package from Bioconductor. The code should look like the following and include eval = FALSE.

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("cosmosR")

[ ] SUGGESTION: We strongly encourage the use of table of contents.

Man pages

[ ] REQUIRED: We don't allow for a figures directory in the man directory. If these figures are needed that they should go in 'inst/figures'.

R code

[ ] REQUIRED: Avoid sapply(); use vapply() were possible. Found in files: display_node_neighborhood.R, lines 49, 56, and 64 filter_pkn_expressed_genes.R, lines 68 and 71 format_COSMOS_results.R, lines 34, 47, 66, 159, 252, 332, 339, and 369
[ ] REQUIRED: Avoid the use of 'paste' in condition signalers. Found in files: check_network_data_coverage.R, lines 40 and 55 cosmos_data.R, lines 140 and 156
[ ] REQUIRED: Avoid redundancy in signalers. Found in files: convert_ensembl_to_entrezid.R, line18
[ ] SUGGESTION: For formating reasons, consider shorter lines. There are 294 lines that are > 80 characters long.
[ ] SUGGESTION: For formating reasons, consider multiples of 4 spaces for line indents. There are 497 lines that are not.

Best, Kayla

Kayla-Morrell commented 3 years ago

@katharinazirngibl - I should have mentioned in my review above to keep in mind that the deadline to accept new packages into the Bioconductor 3.13 release is May 12th. Any packages accepted after this date will be included in the next release.

Best, Kayla

katharinazirngibl commented 3 years ago

Dear Kayla,

thank you very much for your review and your reminder. We are actively working on the package to address the issues that you raised. Regarding the License, does this mean we should simply delete the LICENSE file and that the license stated in the DESCRIPTION file is sufficient?

Kind regards, Katharina

Kayla-Morrell commented 3 years ago

@katharinazirngibl - That's correct, you can just remove the LICENSE file and keep just 'GPL-3' in the DESCRIPTION file.

Best, Kayla

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f4eb97c690950524ea4c2f87ce39c5b3de3c96f5

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/cosmosR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

katharinazirngibl commented 3 years ago

Dear Kayla,

thank you for your help. We made the requested changes to the code and updated the bioconductor git repository. In this new version bump we addressed:

General package development issue: The docs/ directory was removed from the package
DESCRIPTION: The LICENSE file as well as LazyData loading was removed
NEWS: The news file was updated to comply with the formatting requirements
Vignette: The installation section as well as a table of content was added to the vignette
Man page: The figures folder originally located in the man directory was moved to the inst/ directory
R code:
1. 'sapply' was exchanged with 'vapply' wherever possible. 'sapply' is still present in the display_node_neighborhood.R function because the return from igraph depends on the size and complexity of the input network to be plotted and is not predictable. Also five out of the eight 'sapply' in the format_COSMOS_results.R function were kept because they are formatting ENTREZ gene/protein ids from the input network and again, depending on the size of the network the return value of these functions varies.
2. 'paste' was removed from all condition signalers
3. Removed redundancy in signalers

We did not address the code formatting suggestions due to the lack of time. But we will continue to maintain and further develop this package, so we will put it on the list for the next submission in fall!

Thank you very much for your time and the revision, Katharina

Kayla-Morrell commented 3 years ago

@katharinazirngibl - Thank you for making the necessary changes. I have reviewed everything and I'm more than happy to accept the package.

Best, Kayla

bioc-issue-bot commented 3 years ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

vjcitn commented 3 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/katharinazirngibl.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("cosmosR"). The package 'landing page' will be created at

https://bioconductor.org/packages/cosmosR

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

Bioconductor / Contributions

cosmosR #2086

General package development

DESCRIPTION

NEWS

Vignette

Man pages

R code